The unseeded Indian combine lost 3-6 2-6 to the second seeded Croat-Brazilian combo in the quarterfinal, which was over in just 51 minutes.
Paes and Bopanna play with different partners on the ATP tour and hence playing against a formidable team, which has done extremely well this season, was a tall order.
Melo and Dodig reached the US Open semi-finals and also reached finals of two Master series events -- Canada and Monte Carlo -- this year.
Paes and Bopanna had beaten local wild card pair of Tatsuma Ito and Go Soeda in their opening round.